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This page was generated on 2022-01-26 13:06:52 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for MesKit on tokay2


To the developers/maintainers of the MesKit package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MesKit.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1087/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MesKit 1.4.0  (landing page)
Mengni Liu
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/MesKit
git_branch: RELEASE_3_14
git_last_commit: 0782512
git_last_commit_date: 2021-10-26 13:01:22 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MesKit
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MesKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MesKit_1.4.0.tar.gz
StartedAt: 2022-01-25 22:32:42 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 22:45:01 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 739.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MesKit.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MesKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MesKit_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MesKit.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MesKit/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MesKit' version '1.4.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'MesKit' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'ape::degree' by 'circlize::degree' when loading 'MesKit'
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MesKit.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calJSI : processJSI: no visible binding for global variable 'CCF'
cna2gene: no visible global function definition for 'genes'
cna2gene: no visible binding for global variable 'org.Hs.eg.db'
cna2gene: no visible binding for global variable 'seqnames'
cna2gene: no visible binding for global variable 'Chromosome'
cna2gene: no visible binding for global variable 'Hugo_Symbol'
cna2gene: no visible binding for global variable 'Start_Position'
cna2gene: no visible binding for global variable 'End_Position'
cna2gene: no visible binding for global variable 'i.End_Position'
cna2gene: no visible binding for global variable 'i.Start_Position'
cna2gene: no visible binding for global variable 'Patient_ID'
cna2gene: no visible binding for global variable 'Tumor_Sample_Barcode'
cna2gene: no visible binding for global variable 'seg_id'
cna2gene: no visible binding for global variable 'overlap_width'
copyNumberFilter: no visible binding for global variable 'Patient_ID'
drawVAFCombine: no visible binding for global variable 'V'
drawVAFCombineVline: no visible binding for global variable 'V'
fitSignatures : processFitSig: no visible binding for global variable
  'Branch'
fitSignatures : processFitSig: no visible binding for global variable
  'Original'
fitSignatures : processFitSig: no visible binding for global variable
  'Reconstructed'
mutCluster : processVafcluster_sample: no visible binding for global
  variable 'cluster'
plotCNA: no visible binding for global variable 'Cytoband'
plotCNA: no visible binding for global variable 'Cytoband_pos'
plotCNA: no visible binding for global variable 'gene_id'
plotCNA: no visible binding for global variable 'gene_pos'
plotCNA: no visible binding for global variable 'Hugo_Symbol'
plotTree: no visible binding for global variable 'is.match'
plotTree: no visible binding for global variable 'x'
plotTree: no visible binding for global variable 'y'
plotTree: no visible binding for global variable 'xend'
plotTree: no visible binding for global variable 'yend'
Undefined global functions or variables:
  Branch CCF Chromosome Cytoband Cytoband_pos End_Position Hugo_Symbol
  Original Patient_ID Reconstructed Start_Position Tumor_Sample_Barcode
  V cluster gene_id gene_pos genes i.End_Position i.Start_Position
  is.match org.Hs.eg.db overlap_width seg_id seqnames x xend y yend
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
cna2gene             19.44   0.62   20.16
getPhyloTreeTsbLabel 12.08   0.00   12.06
plotMutSigProfile    11.93   0.14   12.06
calFst               11.44   0.48   12.36
getMutBranches       11.12   0.10   11.22
getPhyloTreeRef      10.98   0.00   10.98
getBootstrapValue    10.81   0.12   10.92
getBinaryMatrix      10.75   0.17   10.91
getPhyloTreePatient  10.75   0.00   10.75
getBranchType        10.44   0.05   10.48
getCCFMatrix         10.40   0.08   10.49
getTree              10.28   0.01   10.28
getTreeMethod        10.18   0.02   10.20
getPhyloTree         10.16   0.02   10.17
compareCCF            7.87   0.92    8.80
mutHeatmap            8.08   0.03    8.11
compareTree           6.78   1.19    7.95
calJSI                7.38   0.05    7.39
calNeiDist            7.25   0.04    7.29
fitSignatures         6.46   0.19    6.64
triMatrix             6.15   0.08    6.24
mutCluster            6.10   0.03    6.09
testNeutral           5.88   0.02    5.87
ccfAUC                5.71   0.05    5.71
mutTrunkBranch        5.59   0.03    5.63
plotPhyloTree         5.41   0.03    5.43
plotMutProfile        5.22   0.03    5.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
cna2gene             18.72   0.44   19.15
calFst               12.13   0.16   12.28
getMutBranches       11.14   0.17   11.29
getBinaryMatrix      11.03   0.04   11.06
getTree              11.00   0.00   11.00
getBranchType        10.75   0.00   10.75
getBootstrapValue    10.67   0.04   10.70
getPhyloTreePatient  10.09   0.01   10.11
getTreeMethod        10.08   0.00   10.08
getCCFMatrix          9.94   0.01    9.95
getPhyloTreeRef       9.78   0.02    9.79
getPhyloTreeTsbLabel  9.41   0.01    9.41
getPhyloTree          9.32   0.02    9.33
plotMutSigProfile     8.54   0.13    8.67
calNeiDist            7.78   0.01    7.79
mutHeatmap            7.67   0.02    7.69
compareTree           7.56   0.04    7.65
compareCCF            6.72   0.33    7.03
calJSI                6.86   0.03    6.88
fitSignatures         6.22   0.24    6.46
mutCluster            5.94   0.11    6.04
ccfAUC                5.97   0.04    6.00
plotMutProfile        5.86   0.02    5.86
mutTrunkBranch        5.74   0.04    5.78
plotPhyloTree         5.42   0.00    5.41
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/MesKit.Rcheck/00check.log'
for details.



Installation output

MesKit.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MesKit_1.4.0.tar.gz && rm -rf MesKit.buildbin-libdir && mkdir MesKit.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MesKit.buildbin-libdir MesKit_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MesKit_1.4.0.zip && rm MesKit_1.4.0.tar.gz MesKit_1.4.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1801k  100 1801k    0     0  2606k      0 --:--:-- --:--:-- --:--:-- 2610k

install for i386

* installing *source* package 'MesKit' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'ape::degree' by 'circlize::degree' when loading 'MesKit'
** help
*** installing help indices
  converting help for package 'MesKit'
    finding HTML links ... done
    Maf-class                               html  
    MafList-class                           html  
    calFst                                  html  
    calJSI                                  html  
    calNeiDist                              html  
    ccfAUC                                  html  
    classifyMut                             html  
    cna2gene                                html  
    compareCCF                              html  
    compareTree                             html  
    fitSignatures                           html  
    getBinaryMatrix                         html  
    getBootstrapValue                       html  
    getBranchType                           html  
    getCCFMatrix                            html  
    getMafData                              html  
    getMafPatient                           html  
    getMafRef                               html  
    getMutBranches                          html  
    getNonSyn_vc                            html  
    getPhyloTree                            html  
    getPhyloTreePatient                     html  
    getPhyloTreeRef                         html  
    getPhyloTreeTsbLabel                    html  
    getSampleInfo                           html  
    getTree                                 html  
    getTreeMethod                           html  
    mathScore                               html  
    mutCluster                              html  
    mutHeatmap                              html  
    mutTrunkBranch                          html  
    phyloTree-class                         html  
    phyloTreeList-class                     html  
    plotCNA                                 html  
    plotMutProfile                          html  
    plotMutSigProfile                       html  
    plotPhyloTree                           html  
    readMaf                                 html  
    readSegment                             html  
    runMesKit                               html  
    subMaf                                  html  
    testNeutral                             html  
    triMatrix                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'ape::degree' by 'circlize::degree' when loading 'MesKit'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'ape::degree' by 'circlize::degree' when loading 'MesKit'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'MesKit' ...
** testing if installed package can be loaded
Warning: replacing previous import 'ape::degree' by 'circlize::degree' when loading 'MesKit'
* MD5 sums
packaged installation of 'MesKit' as MesKit_1.4.0.zip
* DONE (MesKit)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MesKit' successfully unpacked and MD5 sums checked

Tests output


Example timings

MesKit.Rcheck/examples_i386/MesKit-Ex.timings

nameusersystemelapsed
calFst11.44 0.4812.36
calJSI7.380.057.39
calNeiDist7.250.047.29
ccfAUC5.710.055.71
classifyMut3.710.023.74
cna2gene19.44 0.6220.16
compareCCF7.870.928.80
compareTree6.781.197.95
fitSignatures6.460.196.64
getBinaryMatrix10.75 0.1710.91
getBootstrapValue10.81 0.1210.92
getBranchType10.44 0.0510.48
getCCFMatrix10.40 0.0810.49
getMafData3.330.003.31
getMafPatient3.170.023.19
getMafRef3.240.003.23
getMutBranches11.12 0.1011.22
getNonSyn_vc3.000.002.99
getPhyloTree10.16 0.0210.17
getPhyloTreePatient10.75 0.0010.75
getPhyloTreeRef10.98 0.0010.98
getPhyloTreeTsbLabel12.08 0.0012.06
getSampleInfo2.850.022.85
getTree10.28 0.0110.28
getTreeMethod10.18 0.0210.20
mathScore3.140.033.16
mutCluster6.100.036.09
mutHeatmap8.080.038.11
mutTrunkBranch5.590.035.63
plotCNA3.080.023.09
plotMutProfile5.220.035.25
plotMutSigProfile11.93 0.1412.06
plotPhyloTree5.410.035.43
readMaf4.090.054.10
readSegment0.440.030.49
runMesKit000
subMaf3.530.013.55
testNeutral5.880.025.87
triMatrix6.150.086.24

MesKit.Rcheck/examples_x64/MesKit-Ex.timings

nameusersystemelapsed
calFst12.13 0.1612.28
calJSI6.860.036.88
calNeiDist7.780.017.79
ccfAUC5.970.046.00
classifyMut3.970.013.96
cna2gene18.72 0.4419.15
compareCCF6.720.337.03
compareTree7.560.047.65
fitSignatures6.220.246.46
getBinaryMatrix11.03 0.0411.06
getBootstrapValue10.67 0.0410.70
getBranchType10.75 0.0010.75
getCCFMatrix9.940.019.95
getMafData3.190.003.19
getMafPatient3.140.003.14
getMafRef3.300.023.32
getMutBranches11.14 0.1711.29
getNonSyn_vc3.040.033.08
getPhyloTree9.320.029.33
getPhyloTreePatient10.09 0.0110.11
getPhyloTreeRef9.780.029.79
getPhyloTreeTsbLabel9.410.019.41
getSampleInfo3.530.003.53
getTree11 011
getTreeMethod10.08 0.0010.08
mathScore3.180.003.19
mutCluster5.940.116.04
mutHeatmap7.670.027.69
mutTrunkBranch5.740.045.78
plotCNA2.570.002.56
plotMutProfile5.860.025.86
plotMutSigProfile8.540.138.67
plotPhyloTree5.420.005.41
readMaf3.130.003.11
readSegment0.590.000.59
runMesKit000
subMaf3.330.003.33
testNeutral4.840.004.86
triMatrix4.900.074.97